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- PDB-7b37: Notum complex with ARUK3003718 -

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Basic information

Entry
Database: PDB / ID: 7b37
TitleNotum complex with ARUK3003718
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor
Function / homology
Function and homology information


protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway ...protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region
Similarity search - Function
Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
Chem-SRK / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsZhao, Y. / Jone, E.Y.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Insights into Notum Covalent Inhibition.
Authors: Zhao, Y. / Svensson, F. / Steadman, D. / Frew, S. / Monaghan, A. / Bictash, M. / Moreira, T. / Chalk, R. / Lu, W. / Fish, P.V. / Jones, E.Y.
History
DepositionNov 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,75012
Polymers43,5671
Non-polymers1,18311
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-32 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.163, 71.546, 78.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Palmitoleoyl-protein carboxylesterase NOTUM / hNOTUM


Mass: 43567.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Production host: Homo sapiens (human)
References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 100 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SRK / 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid


Mass: 219.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 4.2 / Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.34→78.12 Å / Num. obs: 76452 / % possible obs: 100 % / Redundancy: 50.5 % / CC1/2: 1 / Net I/σ(I): 21.1
Reflection shellResolution: 1.34→1.36 Å / Num. unique obs: 3720 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ARG

7arg


Resolution: 1.34→46.05 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 3814 4.99 %
Rwork0.1926 72555 -
obs0.1931 76369 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.41 Å2 / Biso mean: 20.9722 Å2 / Biso min: 11.73 Å2
Refinement stepCycle: final / Resolution: 1.34→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 70 90 2930
Biso mean--30.93 24.01 -
Num. residues----346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.34-1.360.23061450.25172611275699
1.36-1.370.21161440.246326672811100
1.37-1.390.25291500.231226362786100
1.39-1.410.24491360.228426502786100
1.41-1.430.21631270.212826872814100
1.43-1.460.21411440.201826562800100
1.46-1.480.20991390.202126412780100
1.48-1.510.23111280.192126882816100
1.51-1.530.21951340.193626472781100
1.53-1.560.19351490.178726702819100
1.56-1.590.18011310.175726672798100
1.59-1.630.17561460.182226722818100
1.63-1.670.19761260.178526952821100
1.67-1.710.22031370.175526562793100
1.71-1.760.18391300.181826702800100
1.76-1.810.23771380.176426812819100
1.81-1.870.18451420.180326922834100
1.87-1.930.20111470.186426822829100
1.93-2.010.22611350.176726792814100
2.01-2.10.19711490.177526822831100
2.1-2.210.18161280.178727052833100
2.21-2.350.19611480.189527042852100
2.35-2.530.21481340.192827312865100
2.53-2.790.20941540.199227002854100
2.79-3.190.20141430.201827482891100
3.19-4.020.19021650.193627422907100
4.02-46.050.20431650.198828963061100
Refinement TLS params.Method: refined / Origin x: 25.5659 Å / Origin y: 70.3646 Å / Origin z: 80.593 Å
111213212223313233
T0.1314 Å2-0.004 Å2-0.0039 Å2-0.1487 Å2-0.0143 Å2--0.1353 Å2
L0.6909 °2-0.0674 °2-0.124 °2-0.9428 °2-0.054 °2--0.6387 °2
S-0.0054 Å °-0.0121 Å °0.0221 Å °-0.0055 Å °0.0002 Å °0.0116 Å °-0.0404 Å °0.014 Å °0.0119 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA87 - 2501
2X-RAY DIFFRACTION1allS2 - 233
3X-RAY DIFFRACTION1allB1

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